BAFsegmented file not always sorted in chromosomal order

[sdentro]

Had a report that the BAFsegmented file was not sorted properly. This results in the chromosomes getting jumbled during fitcopynumber and callsubclones. It's unclear what the cause is, but a fix is to sort the dataframe at the end of segmentation to preserve the correct order.

[keiranmraine]

@sdentro, is this resolved by your recent changes it's not clear from the commit messages. If so can you point me to the relevant commit?

Thanks

[sdentro]

@keiranmraine No this is still an open issue. It might be due to a
different order of the chromosomes in the impute_info.txt file. But
haven't come around to test this. Otherwise fixing this issue is just
sorting the chromosome names before the for loop such that the segmented
data is concatenated correctly

On 28/01/2016 16:21, Keiran Raine wrote:

@sdentro https://github.com/sdentro, is this resolved by your recent
changes it's not clear from the commit messages. If so can you point
me to the relevant commit?

Thanks

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